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Han J, Ritchey B, Opoku E, Smith JD. Fine Mapping of the Mouse Ath28 Locus Yields Three Atherosclerosis Modifying Sub-Regions. Genes (Basel) 2021; 13:70. [PMID: 35052410 PMCID: PMC8774523 DOI: 10.3390/genes13010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
A mouse strain intercross between Apoe-/- AKR/J and DBA/2J mice identified three replicated atherosclerosis quantitative trait loci (QTLs). Our objective was to fine map mouse atherosclerosis modifier genes within a genomic region known to affect lesion development in apoE-deficient (Apoe-/-) mice. We dissected the Ath28 QTL on the distal end of chromosome 2 by breeding a panel of congenic strains and measuring aortic root lesion area in 16-week-old male and female mice fed regular laboratory diets. The parental congenic strain contained ~9.65 Mb of AKR/J DNA from chromosome 2 on the DBA/2J genetic background, which had lesions 55% and 47% smaller than female and male DBA/2J mice, respectively (p < 0.001). Seven additional congenic lines identified three separate regions associated with the lesion area, named Ath28.1, Ath28.2, and Ath28.3, where the AKR/J alleles were atherosclerosis-protective for two regions and atherosclerosis-promoting for the other region. These results were replicated in both sexes, and in combined analysis after adjusting for sex. The congenic lines did not greatly impact total and HDL cholesterol levels or body weight. Bioinformatic analyses identified all coding and non-coding genes in the Ath28.1 sub-region, as well as strain sequence differences that may be impactful. Even within a <10 Mb region of the mouse genome, evidence supports the presence of at least three atherosclerosis modifier genes that differ between the AKR/J and DBA/2J mouse strains, supporting the polygenic nature of atherosclerosis susceptibility.
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Affiliation(s)
| | | | | | - Jonathan D. Smith
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA; (J.H.); (B.R.); (E.O.)
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Ritchey B, Hai Q, Han J, Barnard J, Smith JD. Genetic variant in 3' untranslated region of the mouse pycard gene regulates inflammasome activity. eLife 2021; 10:e68203. [PMID: 34197316 PMCID: PMC8248980 DOI: 10.7554/elife.68203] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Quantitative trait locus mapping for interleukin-1β release after inflammasome priming and activation was performed on bone-marrow-derived macrophages (BMDM) from an AKRxDBA/2 mouse strain intercross. The strongest associated locus mapped very close to the Pycard gene on chromosome 7, which codes for the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC). The DBA/2 and AKR Pycard genes only differ at a single-nucleotide polymorphism (SNP) in their 3' untranslated region (UTR). DBA/2 vs. AKR BMDM had increased levels of Pycard mRNA expression and ASC protein, and increased inflammasome speck formation, which was associated with increased Pycard mRNA stability without an increased transcription rate. CRISPR/Cas9 gene editing was performed on DBA/2 embryonic stem cells to change the Pycard 3'UTR SNP from the DBA/2 to the AKR allele. This single base change significantly reduced Pycard expression and inflammasome activity after cells were differentiated into macrophages due to reduced Pycard mRNA stability.
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Affiliation(s)
- Brian Ritchey
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Qimin Hai
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Juying Han
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
| | - Jonathan D Smith
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland ClinicClevelandUnited States
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve UniversityClevelandUnited States
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Quantitative trait locus mapping identifies the Gpnmb gene as a modifier of mouse macrophage lysosome function. Sci Rep 2021; 11:10249. [PMID: 33986446 PMCID: PMC8119501 DOI: 10.1038/s41598-021-89800-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/30/2021] [Indexed: 01/28/2023] Open
Abstract
We have previously shown that the DBA/2J versus AKR/J mouse strain is associated with decreased autophagy-mediated lysosomal hydrolysis of cholesterol esters. Our objective was to determine differences in lysosome function in AKR/J and DBA/2J macrophages, and identify the responsible genes. Using a novel dual-labeled indicator of lysosome function, DBA/2J versus AKR/J bone marrow derived macrophages had significantly decreased lysosome function. We performed quantitative trait loci mapping of lysosome function in bone marrow macrophages from an AKR/J × DBA/2J strain intercross. Four distinct lysosome function loci were identified, which we named macrophage lysosome function modifier (Mlfm) Mlfm1 through Mlfm4. The strongest locus Mlfm1 harbors the Gpnmb gene, which has been shown to recruit autophagy protein light chain 3 to autophagosomes for lysosome fusion. The parental DBA/2J strain has a nonsense variant in Gpnmb. siRNA knockdown of Gpnmb in AKR/J macrophages decreased lysosome function, and Gpnmb deletion through CRISP/Cas9 editing in RAW 264.7 mouse macrophages also demonstrated a similar result. Furthermore, a DBA/2 substrain, called DBA/2J-Gpnmb+/SjJ, contains the wildtype Gpnmb gene, and macrophages from this Gpnmb-preserved DBA/2 substrain exhibited recovered lysosome function. In conclusion, we identified Gpnmb as a causal modifier gene of lysosome function in this strain pair.
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Kim M, Huda MN, O'Connor A, Albright J, Durbin-Johnson B, Bennett BJ. Hepatic transcriptional profile reveals the role of diet and genetic backgrounds on metabolic traits in female progenitor strains of the Collaborative Cross. Physiol Genomics 2021; 53:173-192. [PMID: 33818129 PMCID: PMC8424536 DOI: 10.1152/physiolgenomics.00140.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/28/2022] Open
Abstract
Mice have provided critical mechanistic understandings of clinical traits underlying metabolic syndrome (MetSyn) and susceptibility to MetSyn in mice is known to vary among inbred strains. We investigated the diet- and strain-dependent effects on metabolic traits in the eight Collaborative Cross (CC) founder strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Liver transcriptomics analysis showed that both atherogenic diet and host genetics have profound effects on the liver transcriptome, which may be related to differences in metabolic traits observed between strains. We found strain differences in circulating trimethylamine N-oxide (TMAO) concentration and liver triglyceride content, both of which are traits associated with metabolic diseases. Using a network approach, we identified a module of transcripts associated with TMAO and liver triglyceride content, which was enriched in functional pathways. Interrogation of the module related to metabolic traits identified NADPH oxidase 4 (Nox4), a gene for a key enzyme in the production of reactive oxygen species, which showed a strong association with plasma TMAO and liver triglyceride. Interestingly, Nox4 was identified as the highest expressed in the C57BL/6J and NZO/HILtJ strains and the lowest expressed in the CAST/EiJ strain. Based on these results, we suggest that there may be genetic variation in the contribution of Nox4 to the regulation of plasma TMAO and liver triglyceride content. In summary, we show that liver transcriptomic analysis identified diet- or strain-specific pathways for metabolic traits in the Collaborative Cross (CC) founder strains.
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Affiliation(s)
- Myungsuk Kim
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
| | - M Nazmul Huda
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
| | - Annalouise O'Connor
- Nutrition Research Institute, University of North Carolina, Kannapolis, North Carolina
| | - Jody Albright
- Nutrition Research Institute, University of North Carolina, Kannapolis, North Carolina
| | | | - Brian J Bennett
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
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Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene. Atherosclerosis 2019; 286:71-78. [PMID: 31102955 DOI: 10.1016/j.atherosclerosis.2019.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/28/2019] [Accepted: 05/08/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS We previously demonstrated that Apoe-/- mice on DBA/2 vs. AKR genetic background have >10-fold larger atherosclerotic lesions. Prior quantitative trait locus mapping via strain intercrossing identified a region on chromosome 17, Ath26, as the strongest atherosclerosis-modifying locus. We aimed to confirm Ath26, identify candidate genes, and validate the candidate gene effects on atherosclerosis. METHODS We bred chromosome 17 interval congenic mice to confirm that Ath26 locus contains atherosclerosis modifying gene(s). Bone marrow derived macrophage transcriptomics was performed to identify candidate genes at this locus whose expression was correlated with lesions in a strain intercross. The Cyp4f13 candidate gene was tested via a gene knockout approach and in vivo and ex vivo phenotype analyses. RESULTS A congenic mouse strain containing the DBA/2 interval on chromosome 17 on the AKR Apoe-/- background demonstrated that this interval conferred increased lesion area. Transcriptomic analysis of bone marrow macrophages identified that expression of the Cyp4f13 gene, mapping to this locus, was highly associated with lesion area in an F2 cohort. AKR vs. DBA/2 macrophages had less Cyp4f13 mRNA expression, and their livers had lower leukotriene B4 (LTB4) 20-hydroxylase enzymatic activity. A Cyp4f13 knockout allele was bred onto the DBA/2 Apoe-/- background and this conferred less enzymatic activity, decreased macrophage migration in response to LTB4, and smaller aortic root atherosclerotic lesions. CONCLUSIONS Allelic differences in the Cyp4f13 gene may in part be responsible for the Ath26 QTL conferring larger lesions in DBA/2 vs. AKR Apoe-/- mice.
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Han J, Enyindah-Asonye G, Lin F, Smith JD. CD6 expression has no effect on atherosclerosis in apolipoprotein E-deficient mice. BMC Res Notes 2018; 11:229. [PMID: 29615096 PMCID: PMC5883413 DOI: 10.1186/s13104-018-3327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/24/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To determine if deficiency of CD6, a cell surface protein on lymphocytes that alters natural antibody production, increases atherosclerosis in ApoE-deficient mice fed a chow or a western-type diet. RESULTS We compared cholesterol levels, IgM, B1a cells, and aortic root lesion areas in ApoE-deficient vs. CD6/ApoE double deficient mice. Feeding the high-fat western type diet increased all parameters, except for B1a cell numbers decreased. Sex also had an effect on many parameters with males having increased body weights, higher high density lipoprotein cholesterol, higher B1a cells, but smaller atherosclerotic lesions if chow fed mice; however, this sex effect on atherosclerosis was absent in mice fed the western-type diet. CD6 deficiency had no effect on atherosclerosis in both male and female mice on either diet. Thus, loss of CD6 on lymphocytes did not lead to expected reductions in B1a cells and protective IgM levels, and in turn did not alter atherosclerosis in mice.
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Affiliation(s)
- Juying Han
- Department of Cellular & Molecular Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Gospel Enyindah-Asonye
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Feng Lin
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, USA.
| | - Jonathan D Smith
- Department of Cellular & Molecular Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, USA.
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Hai Q, Ritchey B, Robinet P, Alzayed AM, Brubaker G, Zhang J, Smith JD. Quantitative Trait Locus Mapping of Macrophage Cholesterol Metabolism and CRISPR/Cas9 Editing Implicate an ACAT1 Truncation as a Causal Modifier Variant. Arterioscler Thromb Vasc Biol 2017; 38:83-91. [PMID: 29097366 DOI: 10.1161/atvbaha.117.310173] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/19/2017] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Cholesterol metabolism is a dynamic process involving intracellular trafficking, cholesterol esterification, and cholesterol ester hydrolysis. Our objective was to identify genes that regulate macrophage cholesterol metabolism. APPROACHES AND RESULTS We performed quantitative trait loci mapping of free and esterified cholesterol levels and the ratio of esterified to free cholesterol in acetylated low-density lipoprotein-loaded bone marrow-derived macrophages from an AKR×DBA/2 strain intercross. Ten distinct cholesterol modifier loci were identified, and bioinformatics was used to prioritize candidate genes. The strongest locus was located on distal chromosome 1, which we named Mcmm1 (macrophage cholesterol metabolism modifier 1). This locus harbors the Soat1 (sterol O-acyltransferase 1) gene, encoding Acyl-coenzyme A:cholesterol acyltransferase 1 (ACAT1), which esterifies free cholesterol. The parental AKR strain has an exon 2 deletion in Soat1, which leads to a 33 amino acid N-terminal truncation in ACAT1. CRISPR/Cas9 editing of DBA/2 embryonic stem cells was performed to replicate the AKR strain Soat1 exon 2 deletion, while leaving the remainder of the genome unaltered. DBA/2 stem cells and stem cells heterozygous and homozygous for the Soat1 exon 2 deletion were differentiated into macrophages and loaded with acetylated low-density lipoprotein. DBA/2 stem cell-derived macrophages accumulated less free cholesterol and more esterified cholesterol relative to cells heterozygous and homozygous for the Soat1 exon 2 deletion. CONCLUSIONS A Soat1 deletion present in AKR mice, and resultant N-terminal ACAT1 truncation, was confirmed to be a significant modifier of macrophage cholesterol metabolism. Other Mcmm loci candidate genes were prioritized via bioinformatics.
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Affiliation(s)
- Qimin Hai
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.)
| | - Brian Ritchey
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.)
| | - Peggy Robinet
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.)
| | - Alexander M Alzayed
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.)
| | - Greg Brubaker
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.)
| | - Jinying Zhang
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.).
| | - Jonathan D Smith
- From the Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Henan, China (Q.H., J.Z.); Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland, OH (Q.H., B.R., P.R., A.M.A., G.B., J.D.S); and Department of Chemistry, Cleveland State University, OH (B.R.).
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Common, low-frequency, and rare genetic variants associated with lipoprotein subclasses and triglyceride measures in Finnish men from the METSIM study. PLoS Genet 2017; 13:e1007079. [PMID: 29084231 PMCID: PMC5679656 DOI: 10.1371/journal.pgen.1007079] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/09/2017] [Accepted: 10/16/2017] [Indexed: 12/12/2022] Open
Abstract
Lipid and lipoprotein subclasses are associated with metabolic and cardiovascular diseases, yet the genetic contributions to variability in subclass traits are not fully understood. We conducted single-variant and gene-based association tests between 15.1M variants from genome-wide and exome array and imputed genotypes and 72 lipid and lipoprotein traits in 8,372 Finns. After accounting for 885 variants at 157 previously identified lipid loci, we identified five novel signals near established loci at HIF3A, ADAMTS3, PLTP, LCAT, and LIPG. Four of the signals were identified with a low-frequency (0.005<minor allele frequency [MAF]<0.05) or rare (MAF<0.005) variant, including Arg123His in LCAT. Gene-based associations (P<10-10) support a role for coding variants in LIPC and LIPG with lipoprotein subclass traits. 30 established lipid-associated loci had a stronger association for a subclass trait than any conventional trait. These novel association signals provide further insight into the molecular basis of dyslipidemia and the etiology of metabolic disorders.
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von Scheidt M, Zhao Y, Kurt Z, Pan C, Zeng L, Yang X, Schunkert H, Lusis AJ. Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis. Cell Metab 2017; 25:248-261. [PMID: 27916529 PMCID: PMC5484632 DOI: 10.1016/j.cmet.2016.11.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/26/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022]
Abstract
Most of the biological understanding of mechanisms underlying coronary artery disease (CAD) derives from studies of mouse models. The identification of multiple CAD loci and strong candidate genes in large human genome-wide association studies (GWASs) presented an opportunity to examine the relevance of mouse models for the human disease. We comprehensively reviewed the mouse literature, including 827 literature-derived genes, and compared it to human data. First, we observed striking concordance of risk factors for atherosclerosis in mice and humans. Second, there was highly significant overlap of mouse genes with human genes identified by GWASs. In particular, of the 46 genes with strong association signals in CAD GWASs that were studied in mouse models, all but one exhibited consistent effects on atherosclerosis-related phenotypes. Third, we compared 178 CAD-associated pathways derived from human GWASs with 263 from mouse studies and observed that the majority were consistent between the species.
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Affiliation(s)
- Moritz von Scheidt
- Deutsches Herzzentrum München, Technische Universität München, 80333 Munich, Germany
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zeyneb Kurt
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calvin Pan
- Departments of Medicine, Microbiology, and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Technische Universität München, 80333 Munich, Germany
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, 80333 Munich, Germany; Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany
| | - Aldons J Lusis
- Departments of Medicine, Microbiology, and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Affiliation(s)
- Jonathan D Smith
- From the Department of Cellular & Molecular Medicine, Cleveland Clinic, OH
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Bennett BJ, Davis RC, Civelek M, Orozco L, Wu J, Qi H, Pan C, Packard RRS, Eskin E, Yan M, Kirchgessner T, Wang Z, Li X, Gregory JC, Hazen SL, Gargalovic PS, Lusis AJ. Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains. PLoS Genet 2015; 11:e1005711. [PMID: 26694027 PMCID: PMC4687930 DOI: 10.1371/journal.pgen.1005711] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/06/2015] [Indexed: 12/15/2022] Open
Abstract
Common forms of atherosclerosis involve multiple genetic and environmental factors. While human genome-wide association studies have identified numerous loci contributing to coronary artery disease and its risk factors, these studies are unable to control environmental factors or examine detailed molecular traits in relevant tissues. We now report a study of natural variations contributing to atherosclerosis and related traits in over 100 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP). The mice were made hyperlipidemic by transgenic expression of human apolipoprotein E-Leiden (APOE-Leiden) and human cholesteryl ester transfer protein (CETP). The mice were examined for lesion size and morphology as well as plasma lipid, insulin and glucose levels, and blood cell profiles. A subset of mice was studied for plasma levels of metabolites and cytokines. We also measured global transcript levels in aorta and liver. Finally, the uptake of acetylated LDL by macrophages from HMDP mice was quantitatively examined. Loci contributing to the traits were mapped using association analysis, and relationships among traits were examined using correlation and statistical modeling. A number of conclusions emerged. First, relationships among atherosclerosis and the risk factors in mice resemble those found in humans. Second, a number of trait-loci were identified, including some overlapping with previous human and mouse studies. Third, gene expression data enabled enrichment analysis of pathways contributing to atherosclerosis and prioritization of candidate genes at associated loci in both mice and humans. Fourth, the data provided a number of mechanistic inferences; for example, we detected no association between macrophage uptake of acetylated LDL and atherosclerosis. Fifth, broad sense heritability for atherosclerosis was much larger than narrow sense heritability, indicating an important role for gene-by-gene interactions. Sixth, stepwise linear regression showed that the combined variations in plasma metabolites, including LDL/VLDL-cholesterol, trimethylamine N-oxide (TMAO), arginine, glucose and insulin, account for approximately 30 to 40% of the variation in atherosclerotic lesion area. Overall, our data provide a rich resource for studies of complex interactions underlying atherosclerosis. While recent genetic association studies in human populations have succeeded in identifying genetic loci that contribute to coronary artery disease (CAD) and related phenotypes, these loci explain only a small fraction of the genetic variation in CAD and associated traits. Here, we present a complementary approach using association analysis of atherosclerotic traits among inbred strains of mice. A strength of this approach is that it enables in-depth phenotypic characterization including gene expression and metabolic profiling across a variety of tissues, and integration of these molecular phenotypes with coronary artery disease itself. A striking finding was the large fraction of atherosclerosis that was explained by genetic interactions. Association analysis allowed us to identify genetic loci for atherosclerotic lesion area as well as transcript, cytokine and metabolite levels, and relationships among the traits were examined by correlation and network modeling. The plasma metabolites associated with atherosclerosis in mice, namely, LDL/VLDL-cholesterol, TMAO, arginine, glucose and insulin, overlapped with those observed in humans and accounted for approximately 30 to 40% of the observed variation in atherosclerotic lesion area. In summary, our data provide a detailed overview of the genetic architecture of atherosclerosis in mice and a rich resource for studies of the complex genetic and metabolic interactions that underlie the disease.
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Affiliation(s)
- Brian J. Bennett
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Richard C. Davis
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Mete Civelek
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Luz Orozco
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Judy Wu
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Hannah Qi
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Calvin Pan
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - René R. Sevag Packard
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Mujing Yan
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Todd Kirchgessner
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Xinmin Li
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Jill C. Gregory
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Stanley L. Hazen
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Peter S. Gargalovic
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Aldons J. Lusis
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Spiezio SH, Amon LM, McMillen TS, Vick CM, Houston BA, Caldwell M, Ogimoto K, Morton GJ, Kirk EA, Schwartz MW, Nadeau JH, LeBoeuf RC. Genetic determinants of atherosclerosis, obesity, and energy balance in consomic mice. Mamm Genome 2014; 25:549-63. [PMID: 25001233 DOI: 10.1007/s00335-014-9530-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/11/2014] [Indexed: 12/18/2022]
Abstract
Metabolic diseases such as obesity and atherosclerosis result from complex interactions between environmental factors and genetic variants. A panel of chromosome substitution strains (CSSs) was developed to characterize genetic and dietary factors contributing to metabolic diseases and other biological traits and biomedical conditions. Our goal here was to identify quantitative trait loci (QTLs) contributing to obesity, energy expenditure, and atherosclerosis. Parental strains C57BL/6 and A/J together with a panel of 21 CSSs derived from these progenitors were subjected to chronic feeding of rodent chow and atherosclerotic (females) or diabetogenic (males) test diets, and evaluated for a variety of metabolic phenotypes including several traits unique to this report, namely fat pad weights, energy balance, and atherosclerosis. A total of 297 QTLs across 35 traits were discovered, two of which provided significant protection from atherosclerosis, and several dozen QTLs modulated body weight, body composition, and circulating lipid levels in females and males. While several QTLs confirmed previous reports, most QTLs were novel. Finally, we applied the CSS quantitative genetic approach to energy balance, and identified three novel QTLs controlling energy expenditure and one QTL modulating food intake. Overall, we identified many new QTLs and phenotyped several novel traits in this mouse model of diet-induced metabolic diseases.
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Affiliation(s)
- Sabrina H Spiezio
- Institute for Systems Biology, 401 North Terry Ave, Seattle, WA, 98109, USA
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Kayashima Y, Tomita H, Zhilicheva S, Kim S, Kim HS, Bennett BJ, Maeda N. Quantitative trait loci affecting atherosclerosis at the aortic root identified in an intercross between DBA2J and 129S6 apolipoprotein E-null mice. PLoS One 2014; 9:e88274. [PMID: 24586312 PMCID: PMC3930552 DOI: 10.1371/journal.pone.0088274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/09/2014] [Indexed: 12/23/2022] Open
Abstract
Apolipoprotein E-null mice on a DBA/2J genetic background (DBA-apoE) are highly susceptible to atherosclerosis in the aortic root area compared with those on a 129S6 background (129-apoE). To explore atherosclerosis-responsible genetic regions, we performed a quantitative trait locus (QTL) analysis using 172 male and 137 female F2 derived from an intercross between DBA-apoE and 129-apoE mice. A genome-wide scan identified two significant QTL for the size of lesions at the root: one is Ath44 on Chromosome (Chr) 1 at 158 Mb, and the other Ath45 on Chr 2 at 162 Mb. Ath44 co-localizes with but appears to be independent of a previously reported QTL, Ath1, while Ath45 is a novel QTL. DBA alleles of both Ath44 and Ath45 confer atherosclerosis-susceptibility. In addition, a QTL on Chr 14 at 73 Mb was found significant only in males, and 129 allele conferring susceptibility. Further analysis detected female-specific interactions between a second QTL on Chr 1 at 73 Mb and a QTL on Chr 3 at 21 Mb, and between Chr 7 at 84 Mb and Chr 12 at 77 Mb. These loci for the root atherosclerosis were independent of QTLs for plasma total cholesterol and QTLs for triglycerides, but a QTL for HDL (Chr 1 at 126 Mb) overlapped with the Ath44. Notably, haplotype analysis among 129S6, DBA/2J and C57BL/6 genomes and their gene expression data narrowed the candidate regions for Ath44 and Ath45 to less than 5 Mb intervals where multiple genome wide associations with cardiovascular phenotypes have also been reported in humans. SNPs in or near Fmo3, Sele and Selp for Ath44, and Lbp and Pkig for Ath45 were suggested for further investigation as potential candidates underlying the atherosclerosis susceptibility.
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Affiliation(s)
- Yukako Kayashima
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hirofumi Tomita
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Svetlana Zhilicheva
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shinja Kim
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hyung-Suk Kim
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brian J. Bennett
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nobuyo Maeda
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Berisha SZ, Hsu J, Robinet P, Smith JD. Transcriptome analysis of genes regulated by cholesterol loading in two strains of mouse macrophages associates lysosome pathway and ER stress response with atherosclerosis susceptibility. PLoS One 2013; 8:e65003. [PMID: 23705026 PMCID: PMC3660362 DOI: 10.1371/journal.pone.0065003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Cholesterol loaded macrophages in the arterial intima are the earliest histological evidence of atherosclerosis. Studies of mouse models of atherosclerosis have shown that the strain background can have a significant effect on lesion development. We have previously shown that DBA/2 ApoE(-/-) mice have aortic root lesions 10-fold larger than AKR ApoE(-/-) mice. The current study analyzes the response to cholesterol loading of macrophages from these two strains. Macrophages from the atherosclerosis susceptible DBA/2 strain had significantly higher levels of total and esterified cholesterol compared to atherosclerosis resistant AKR macrophages, while free cholesterol levels were higher in AKR cells. Gene expression profiles were obtained and data were analyzed for strain, cholesterol loading, and strain-cholesterol loading interaction effects by a fitted linear model. Pathway and transcriptional motif enrichment were identified by gene set enrichment analysis. In addition to observed strain differences in basal gene expression, we identified many transcripts whose expression was significantly altered in response to cholesterol loading, including P2ry13 and P2ry14, Trib3, Hyal1, Vegfa, Ccr5, Ly6a, and Ifit3. Eight pathways were significantly enriched in transcripts regulated by cholesterol loading, among which the lysosome and cytokine-cytokine receptor interaction pathways had the highest number of significantly regulated transcripts. Of the differentially regulated transcripts with a strain-cholesterol loading interaction effect, we identified three genes known to participate in the endoplasmic reticulum (ER) stress response, Ddit3, Trib3 and Atf4. These three transcripts were highly up-regulated by cholesterol in AKR and either down-regulated or unchanged in loaded DBA/2 macrophages, thus associating a robust ER stress response with atherosclerosis resistance. We identified significant transcripts with strain, loading, or strain-loading interaction effect that reside within previously described quantitative trait loci as atherosclerosis modifier candidate genes. In conclusion, we characterized several strain and cholesterol induced differences that may lead to new insights into cellular cholesterol metabolism and atherosclerosis.
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Affiliation(s)
- Stela Z. Berisha
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Jeffrey Hsu
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Peggy Robinet
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Jonathan D. Smith
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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